Waiting for a sign
by johnliz4ever
Summary: John's waiting. Still waiting. Spolier for 'The Eye'. JohnLiz LizAiden. Rating changed to PG13 for content in later chapters.
1. Chapter 1

Disclaimer: I do not own Stargate Atlantis

Note: Do you know that feeing? You know the one I'm talking about. The one where you have no reason for writing. I have no idea why I have this feeling, I just have to write this. I don't even know where it's going. Bare with me.

John came onto the balcony. He lent against the railing. She was gone and there was nothing he could do about. He'd lost her. She wasn't coming back. None of them were coming back. Because of the Genii. So now, he watched, waiting, but for what, he didn't know. He just knew that he would always be waiting. For the time they were reunited. If they'd be reunited.

The door to the balcony opened. Elizabeth stood at the doorway. She didn't know what she expected. She knew he wouldn't be here. She wiped a tear from her eye. A hand placed itself on her shoulder. It was Aiden.

"Elizabeth, the Puddle Jumper is ready."

She nodded.

"I'll be right there."

Aiden nodded and left her, she took one last look out to the balcony before leaving.

She entered the Puddle Jumper and it flew high above the ocean. He wanted his ashes committed to the ocean, the ocean he loved so much. He wanted Elizabeth to spread his ashes there. He made her promise, she'd honour that promise.

The Jumper lost acceleration and dropped just over the water. The back of the Jumper opened. Elizabeth walked over to the back and carefully opened the vase; she spread his ashes, slightly crying as she did. Aiden placed his arms around her. Elizabeth looked to her side. Rodney was gently holding Teyla as she cried. He was trying to hide his own tears but failing. Elizabeth relaxed into Aiden's arms. She'd been strong since it happened. She couldn't be strong anymore.

John was still stood on the balcony. Still waiting for a sign, he didn't know what sign but he knew he know it when he saw it. John heard a noise. He turned, he saw her. His sign. His Elizabeth. She just walked right through him. That's when he realised. When she passed through him and lent on the balcony crying. That's when he knew.

Fin…

I really hope that made sense. For the record, John is a ghost. He's dead. Just an idea, while reading this (If you have it) listen to 'Sacrifice' from Buffy episode 'The Gift'. It might just me but I just think this song works well with it.


	2. Chapter 2

Disclaimer: I don't own Stargate Atlantis

Note: You must all know by now that when I put 'Fin…' at the end of a piece of writing what I'm really putting is 'Fin, until I come up with something else…' and that's what happened this time. Again. Well hear goes nothing.

Spoiler: The Eye. What if Ford, Teyla and Beckett went to the wrong generator?

4 Months later

Elizabeth walked out of her quarters and down the corridors of Atlantis. She placed her hand to the chains around her neck. John's tags now replaced the necklace given to her by Simon. She knew people thought she was mad for wearing them. But it kept her close to John. She had walked into the control room where the night shift were working, Peter among them. Peter was concerned about, as was everybody. They all knew how close they'd been. Even if they feelings for each other were never admitted.

She walked out onto the balcony. She spent a lot of her time there now. She felt his presence there. She quickly wiped away a tear which had formed in her eye. Elizabeth shivered as the door to the balcony opened, Aiden walked out. She was worrying him. She was worrying everyone, but especially him. He placed his jacket around her arms and pulled her into a hug.

Elizabeth shivered more as Aiden held her. Being this close to him felt wrong somehow. That time they had sex felt very wrong. Two months ago. That's when it happened. They were both upset; both needed comfort. That didn't excuse it however. Elizabeth felt uncomfortable now. For crying out loud, he was John's best friend.

Aiden knew how she felt, but try as he might, he couldn't stop his own feelings about her. Even if she never felt anything for him, he knew he'd always feel something for her and he felt terrible about that, because it felt like he was disrespecting John's memory. He'd slept with the women his CO had feelings for.

John watched her, as always, when she slipped onto the balcony. He saw her place her hand on his tags, which now hung from her neck. Since John had realised the truth, it had been very unsettling for him. Knowing he was dead but for some reason, not being able to leave Atlantis. Truth be told, he didn't want to leave, he didn't want to leave her, his Elizabeth. He knew the pain she was going through. He knew she'd slept with Aiden, he knew almost everything that had happened Atlantis since he died, but it didn't matter to him. Nothing mattered except being with her again. He'd wait for her.

John watched the scene unfold as Aiden walked out onto the balcony, he watched as he placed his jacket around Elizabeth before slipping her into his arms. John couldn't help but feel jealous. Jealous that Aiden could actually hold her while he was stood there. Not able to know how she felt to hold. How her beat changed. Aiden could know it all.

Aiden pulled away from Elizabeth slightly and placed his lips to her. A small, gently kiss. Something he just needed to do. Elizabeth pulled away from him, she looked into his eyes, she knew this had to stop. She had to crush his feelings for her. She just didn't know how. She turned away from him and walked off the balcony. Aiden sighed and lent on the railing.

TBC…

Yes I will be continuing this story with a flashback.


	3. Chapter 3

Disclaimer: Not mine, never will be

Note: Flashback chapter.

Flashback (The Eye)

John entered generator room and pulled out the component needed to make the generator work again, he connected some wires together and went to put the component in when two guards appeared. With guns

"Stop!"

"Look you're boss wanted me to turn this thing back on…so I think we should do what he says."

"Be quiet.…" The guard activated his radio "Sora we have him."

Sora answered through her radio

"Keep him alive. I'm on my way".

John still had the component in his hand; he was losing time.

"I don't mean to be a bad prisoner or anything but Kolya is going to kill one of my people if I don't get this thing back on in time so…"

The guard walked behind him and put his gun on his back

"Put in the component"

John put in the component and activated the generator.

"Turn round"

John turned round and looked at the guards. Sora walked into the generator room.

"Major Sheppard"

"Sora."

"Where is Teyla Emmagan?"

John shook his head

"Far as I know, mainland"

"Do not lie to me Major."

John rolled his eyes

"I'm not lying, if I was I'd come up with something more creative"

Sora turned to the guard

"Take him to the control room"

Sora spoke into her radio.

"Commander, we have Major Sheppard. We're taking him to the control room"

"Keep him alive, I'll be there in a moment."

The guards pushed John up to the control room. Not being all to gentle about either.

Kolya walked in minutes later with Elizabeth and Rodney. John sighed, relieved, and gave Elizabeth a small smile, which she returned until she saw Kolya's gun on John.

"60 of my men killed Major Sheppard. How do you think I should even that out? I kill could kill 60 of your people"

Kolya looked at Elizabeth

"Or I could just…" He turned his gun to Elizabeth "…kill her"

John saw the look in Kolya's eyes. He knew he wasn't lying.

"Without Elizabeth you will not be able to activate the shield"

"Good point Major"

Kolya pointed his gun back on John.

"You, however…"

Before Kolya could continue there was an explosion followed by gunshots and three of the Genii guards falling. Kolya was caught of guard and hit in the arm with one of Ford's bullets. Kolya didn't waste anytime in fleeing the scene. John seeing Kolya tying to escape followed him.

Kolya was fast, John was faster. He followed Kolya down the stairs and onto the Gate level.

"Kolya there's no-way for you to go."

He was right; he was backed into a corner. No weapons, bleeding from the wound in his arm.

"Maybe not Major, but there is no-one for you to go either."

Kolya smirked. One of the Genii soldiers was stood behind John, gun on him.

"Give my regards to the Ancients, Major Sheppard."

John heard the shot; he was too slow to react. The bullet pierced him through the back, slowly making it's way through his body. Through skin, blood and muscle. Powerless to stop it. John fell to the ground, conscious of his surroundings, hearing the Stargate activate, the Genii go through, hearing Elizabeth call out for him. Feeling Ford lift him to his feet and take him up to the control consoles. He heard the shield activating, but he couldn't do anything. It hurt too much to move. He sensed a hand take his. Elizabeth's hand. Her heard her prays. He was quiet for the most part. But needed something from her.

"Liz"

Elizabeth's eyes opened.

"John? John oh God, you're going to be okay. I promise."

John managed to shake his head slightly

"No, no I'm not. Liz make me a promise. Spread my ashes over the ocean. I want you to do it."

Tears fell out of Elizabeth's eyes

"Don't, don't say that. Don't you dare die on me. You hear that, it's an order."

"Promise me"

Elizabeth shut her eyes and kissed his forehead

"I promise."

John shut his eyes. He fell in to a sleep slumber, one of which he would never wake up from.

Everyone in the control room became silent and still. The only sound was the storm, which was still happening. The lighten strike, the waves crashed, then all was quiet, all was still.

End of flashback 

TBC…

I will be continuing.


	4. Chapter 4

Disclaimer: I don't own Stargate Atlantis

Note: My English Teacher and my Business Studies Teacher are going to kill me because I'm writing this instead of doing my coursework, but this just will not leave me alone.

Aiden walked through the control room. John followed him. John knew that Aiden had been thinking about the Genii attack. He knew where Aiden was going now. John followed his gaze up to the control room. Elizabeth was there, talking to Peter. As she walked back to her office, her eyes fell over to Aiden but she kept on walking. She closed her door and sat at her laptop.

John looked at Aiden. He knew Aiden's feelings for her. He knew he'd had them for a while, even before John had died he knew about Aiden's feelings for Elizabeth.

But John wanted her for himself. John watched as Aiden made his way up to Elizabeth's office. John thought for a moment. Did he have a right to follow and listen? No, but he'd do it anyway. John quickly followed Aiden up the stairs to Elizabeth's office.

Aiden knocked on Elizabeth's office door, walked in and sat opposite her. She was typing on her laptop; she barely looked up at him. Honestly, because she knew what he was going to say.

"Elizabeth?"

"What can I do for you Lt?"

John saw the begging look in Aiden's eyes

"Elizabeth, please talk to me"

She looked up briefly before looking at the door. She returned her gaze to him.

"Aiden, this is not what I want. I'm sorry if you thought I did. That's my fault. But Aiden, I'm not ready to move on."

"John is dead. I know you had feelings for him, but you've got to move on."

John was slightly shocked at Aiden. He'd never seen Aiden as the 'Move on from your dead love' type. But here he was, asking Elizabeth to forget him. John was, understandably, a little pissed.

Elizabeth shut her laptop and lent forward. She gave Aiden her 'sincere' look.

"Aiden, I know you have feelings for me, you've made that much clear, but I don't have feelings for you. I never have. Maybe one day I might, but that's not today."

John looked at Elizabeth; tears were piercing her eyes. John started to question whether she was telling Aiden the truth. John looked at Aiden. He could tell he was upset and pissed.

"So, why did you sleep with me?"

Elizabeth shook her head

"Aiden, we were both upset, we both still trying to deal with John's death. We found comfort in each other. I never intended for it to lead to anything."

Aiden drummed his fingers against the desk.

"So I was just a substitute for something you couldn't have?"

"I never said that."

"You didn't have to."

Aiden stood up and left the office in a bad temper, which John knew Rodney would be feeling for the rest of the day.

John looked at Elizabeth, her gaze followed Aiden out of the door and down the stairs. The tears that had pierced her eyes had now fallen from them and were running down her cheek. She wiped them away and opened her laptop back up, determined not to let what Aiden said get to her.

_Was it true? Had she used him? Or was there something more?_

TBC…

Hope you're enjoying this so far.


	5. Chapter 5

Disclaimer: Not mine.

Flashback 2 months ago. 

Elizabeth walked through the corridors of Atlantis, before she knew it she was outside John's quarters.

She paused as his door; she ran her finger over it before opening it. She stepped in and saw Aiden. Packing some of John's things.

"Dr Weir."

Aiden was a little startled.

"I was…"

Elizabeth cut him off

"It's okay; truth is I should have done it ages ago."

Aiden nodded and Elizabeth gave him a small smile. Aiden could tell she was broken as she sat on Johns' bed and began folding clothes and placing them in boxes. Aiden watched her actions; they were repetitive. She'd pick something up, fold it, place it in the box, smooth it down then repeat. Aiden had to stop it.

"Do you want to get something to drink?"

Elizabeth turned her head and looked at him and smiled

"Why not?"

Elizabeth got off the bed and followed Aiden to the mess hall.

Ten minutes later, they were both sat down drinking coffee. The mess hall was empty apart from the two of them making the silence unbearable. Elizabeth silently sipped her coffee while Aiden was trying to make conversation.

"Dr Weir are you okay?"

Elizabeth looked up at him and smiled

"Aiden, life is too short for formalities, call me Elizabeth"

Aiden smiled at her

"Are you okay?"

Elizabeth lowered her head and took another sip of her coffee, she didn't know why but it felt as if Aiden could see into her soul through her eyes.

Aiden looked at her, she was trying to build up walls between herself and everyone, she didn't want to risk getting hurt again. Aiden decided he needed to break down those walls, for her own sake. She couldn't stay isolated. It's not healthy. Plus, Aiden had his own reasons for wanting to break down those walls. He had feelings for Elizabeth, he wasn't even sure when these feelings started, he was pretty sure it had been since they came to Atlantis, before that he just saw her as a boss, not a friend. She was different then the others, she was the leader but she was also so real, she had real feelings, real thoughts and she was everything he'd ever wanted. He wanted her to know he was there for her, whenever she wanted or needed him.

"I'm okay"

Elizabeth finally broke the silence and smiled at him, her smile was broken. Elizabeth's smiled usually revealed the real her, but now it was just a mask she put on.

Aiden didn't see it at first but the moment she smiled a tear fell down her cheek, followed by another until finally she couldn't hold them back anymore. The moment he realised she was crying he left his seat, went to Elizabeth and hugged her. Elizabeth hugged him back until he did something quite unexpected. He kissed her.

Elizabeth didn't realise what was happening at first, she didn't realise she was kissing him back. As soon as she realise what they were doing she pulled away from him but not out of his arms. She looked into his eyes; she saw confusion in them. Confusion about what they'd done? Or confusion that she'd pulled back? She didn't know, but she did know she had to put distance between them. She pulled out of Aidens' arms, stood up and left the Mess Hall leaving Aiden thinking about what had just happened.

Aiden sat in the chair that Elizabeth had just left; he buried his head in his hands. He wanted to kiss her, he was glad he did and that was the problem. She wasn't over John, Aiden knew that, but he wanted her for himself. Not to be disrespectful, but John was dead. Aiden stood up and went to his quarters; he was tired. Maybe the whole situation would look different after a good nights sleep.

Aiden walked slowly back to his quarters. He couldn't stop thinking about what had just transpired. Elizabeth must be fairly certain that Aiden felt something for her. He just hoped that it wouldn't ruin their friendship.

Aiden entered his quarters and immediately fell on his bed when he was in reach, he laid their for a few minutes trying to work through the events of the last 30 minutes, otherwise he knew he wouldn't be able to sleep. Finally, he decided that he would go see Elizabeth tomorrow and apologise for kissing her. That was the best thing to do.

Aiden smiled and closed his eyes, until he heard a gentle knock on his door.

Aiden reluctantly stood up and walked to the door, he opened it to reveal an upset Elizabeth.

"Dr Weir are you okay?"

Elizabeth nodded before placing her lips to his, desperately. Aiden didn't resist, he pulled her closer to him and pulled her into his quarters, desperately kissing her back. Elizabeth broke from him and Aidens' lips found their way to her neck.

"Aiden"

Aiden looked at her and brushed his hands through her hair.

"Just relax, let me help you."

Aiden didn't continue, he waited for Elizabeth to make the decision, she placed her lips onto his and Aiden began to kiss her, deepening the kiss.

The next morning

Aiden woke up and instinctively moved his arm to reach for Elizabeth. When he felt nothing but the sheets that lay on his bed, he opened his eyes and scanned round the room. She was gone, any sign she'd been there was gone. Aiden cursed himself.

_What did you expect? Did you expect her to stick around? Or declare her undying love for you?_

_I guess not. I just thought she might have stayed_

_Aiden, John died two months ago. You know how they felt about each other. She wears his tags, that's a big sign. _

_I need to talk to her._

Aiden quickly showered, dressed and made his way to the control room; he knew she'd be there or on the balcony. He knew that about her, he knew when she needed to think she went to the balcony. He slowly realised that in the last two months.

He went to the doors of the balcony and the opened. Elizabeth was there but apparently, she didn't hear the doors open, because she was shocked when Aiden came up next to her. She didn't look at him very long, didn't talk to him. She couldn't. She felt as if she'd just used the poor kid. She did just use him; she used him so she could feel something, anything. She didn't know whether he'd done the same thing or whether it was something more to him and she didn't wait around to find out. She moved away from the railing and left the balcony, leaving Aiden once again, on his own.

End of Flashback

TBC…


	6. Chapter 6

Disclaimer: Don't own Stargate Atlantis.

Two hours later John followed Elizabeth as she walked into the gym. She figured it was were she'd fine Aiden and she was right. He was taking out his anger on a punch-bag that someone had brought with them. Aiden didn't hear her enter. His back was towards her and the sound of his punches were replacing any sound she was making. She walked round to the back of the punch-bag and held it to stop it from swinging. When he saw her, Aiden moved away from the punch-bag and retrieved his things before heading for the door. Elizabeth moved quickly and blocked his way.

"We need to talk"

Aiden looked into her eyes. He _hadn't_ been crying, Lt Ford would not cry. He would get pissed, he would shout, he would take his anger out on any scientist within a five-meter radius, but he would not allow himself to cry.

"No, we really don't. You've made your feelings clear."

Aiden moved to go around her but she blocked his way and grabbed his arm, she stared straight through him, through to his soul.

"We need to talk"

She repeated again. Aiden saw the need in her eyes to discuss what had happened between them. Aiden didn't want to back down but he also knew that he had to listen to her reasoning, for his own sanity.

Aiden moved to the bench near the stain glass window and sat down. Elizabeth followed suit and sat next to him, although not to close. She turned to face him, making eye contact. One of the first things she'd ever learn when she started diplomacy was that to too look sincere and be trusted was to make eye contact and face the person you're talking to. She'd never been so scared of talking to someone in her whole life.

"Aiden, when I left you in the Mess Hall that night I want to Johns' quarters."

Aiden looked away from her; she placed her hands on his cheeks and turned him back to face her.

"No, listen to me…" She ran a hand down his cheek before removing both of them and placing them by her side "…I went to Johns' quarters to think. Think about everything that had happened in those past two months. I thought of all the times you were there for me, all the times you took care of me when I thought I couldn't go on. You were my rock, my strength. You still are. I was thinking, searching for why I kissed you, then it hit me. I felt safe with you, safer then I'd ever felt. I…I felt something for you that night."

John watched as the Elizabeth admitted what had happened to her. He felt numb. Elizabeth was admitting that she actually had felt something for Aiden. John hadn't known that, he'd known about the kiss in the Mess Hall, he was there when she went back to his quarters. He even knew, the next day, that they'd slept together, but not once had John thought her feelings for Aiden went beyond need and comfort.

"I felt something for you and that scared me. I wanted you to comfort me, tell me those feelings were okay. That's why I went to you."

Aiden looked down at his hands; he couldn't deal with the pain that he saw in Elizabeth's eyes. The tears that were forming there. He didn't even realise she held these feelings towards him. He wanted her to, but he never thought she did.

"In the morning, I felt so guilty…for using you the way I did. For using you to feel something. But I've realised the reason I felt guilty was because I did feel something for you and using you for solace was wrong and I was ashamed."

Elizabeth moved her hand to his face and lifted it so he was looking at her again.

"I know you want me to move on, to forget about John, but I can't. I don't know what I'm feeling anymore, about you, about John, about everything. I just need some time to work it out, not a long of time, not forever but it may just take me a while. I just want to know that if we can still be at least civilized to each other."

Aiden nodded his head; he was fighting back the tears.

"Okay"

Elizabeth nodded, stood up and left the gym. Aidens' gaze followed her until she was out of sight.

Being dead meant John didn't have the luxury of crying, Thank God. John had watched the entire encounter between them. John had always known how Aiden felt about Elizabeth, but hearing her say that she felt the same, even if it was just briefly, hurt him more then the bullet that took his life. Maybe he had lost her.

TBC…


	7. Chapter 7

Disclaimer: Don't own Stargate Atlantis.

Note: Last, I think, chapter. I know this chapter will disappoint some people and I know some people will like what I do (I hope). I had to end this story one way or another. Whichever ending I used was sure to disappoint some people, so I chose the one I liked best.

1 Month Later

Just over a month had passed since Elizabeth had talk to Aiden in anything other then the professional capacity. John had spent every waking minute; since he didn't need to sleep he didn't need to leave her, following Elizabeth around Atlantis. Watching her while she slept, trying to decipher her thoughts. He didn't want to leave her side for one moment in fear that he might lose her forever.

As the days slipped away Elizabeth became more and more calm, at peace with herself, over what she done, what she'd felt and it was early that morning when Elizabeth realised what she had to do. Little did she know that Aiden had been thinking as well and he decided on his own course of action.

Elizabeth was standing on the balcony reflecting on what she was going to say to Aiden. She seen him earlier in the day and asked him to stop by the balcony at 3pm. It was now 2.55pm and Elizabeth was still wondering what to say. She'd made her decision earlier in the morning and was certain it was the correct decision. She'd analysed both her feelings for Aiden and her feelings for John and now she knew what she had to do.

The minutes passed rapidly and before she knew it, Aiden entered the balcony. He gave her a small smile, which she returned before gazing back out to the water. Aiden moved over to the balcony and for a few moments, the two of them stood side-by-side gazing over the water, in those few silent moments between them John waited anxiously for their conversation to start. He didn't know what either one of them was going to say and that really pissed him off.

Elizabeth turned to Aiden, who turned around as well. Elizabeths' nerves were starting to get the better of her so she decided to get the conversation over and done with as quickly as possible.

"Aiden…thanks for meeting me." Elizabeth cringed inwardly, that's not how she wanted to start the conversation, but she was going to have to work from that.

"As you know I've been doing some thinking the past month."

_Damn it Elizabeth it's not a negotiation, get to the point_

"Aiden, I've come to a decision. I like you, you're a good friend and a great person and I care for you…but that's all I feel for you."

Johns' head shot up when he heard her. Was she telling him 'no'?

"You deserve someone so much better then me."

Aiden smiled at Elizabeth.

"I've been doing some thinking as well."

John looked suspiciously at Aiden; he didn't seem all that upset.

"I've always known, on some level, what you were going to say to me, and it got me thinking. I like you, but I've realised it is only as a friend. Okay, when we first met I had a major league crush on you, but since I've got to know you, it's changed into friendship, and I don't want to lose that."

John looked between the two of them; he couldn't believe how mature they were being. He was shocked to say the least; he hadn't thought that Aiden would give her up so easy. But then again he hadn't spent much time with Aiden over the past month, he wasn't aware of what he'd been thinking.

Elizabeth and Aiden smiled at each other. Elizabeth cleared her throat

"Friends? Are we both okay with that?"

Aiden smirked

"No"

Elizabeth and John looked at him in confusion

"Lets upgrade that to best friends."

Elizabeth laughed

"Best friends. I can live with that."

They stayed on the balcony a little bit longer until Teyla disturbed them, looking panicked

"Dr Weir, Lt Ford, we have a problem."

Elizabeth turned to face her, she quickly noted the panic on the Athosians' face, it worried Elizabeth

"What kind of problem?"

"Dr McKay is trapped in Jumper one."

Elizabeth and Aiden looked at her in disbelief, the panic immediately fell from Elizabeth and she thought she heard Aiden say something like _'It could only happen to McKay'_ as he walked off the balcony and followed Teyla to the Jumper Bay. Elizabeth gazed back over the ocean thoughtfully for a moment before making her way to the Jumper Bay.

Johns' gaze followed Elizabeth has she left the balcony. He hadn't lost her, it was unbelievable. Johns' feelings surprised him though. Part of him was happy that Elizabeth and Aiden weren't together, but he felt almost sorry for Elizabeth, because she was alone in her life with no-one to love and no-one to loved her, no-one alive anyway. One day that would change, and he hoped that when it did, Elizabeth would be eternally happy. But until that happened John was going to check out the situation in the Jumper Bay because there no chance in Hell he was going to miss Rodney being locked in a Jumper. Johns' eyes fell over the ocean briefly before he left for the Jumper Bay

Fin…


End file.
